Here are 3 other solutions, with a simple tabular, based on the makecell package, which allows for line breaks in column heads:
\documentclass{article}
\usepackage[utf8]{inputenc}
\usepackage[T1]{fontenc}
\usepackage{lmodern}
\usepackage{geometry}%
\usepackage{xspace, array}
\usepackage{booktabs, tabularx, makecell, cellspace}
\usepackage{caption}
\renewcommand\theadfont{\small}
\renewcommand\theadalign{lc}
\setlength\cellspacetoplimit{5pt}
\setlength\cellspacebottomlimit{3pt}
\newcommand\No{N\textsuperscript{o}\xspace}
\begin{document}
\begin{table}[htbp]
\setlength\tabcolsep{4pt}\small
\caption{filter window size}
\label{tab:config_filternum}
\begin{tabular}{|*{3}{Sc|}}
\hline
\thead{\No of entity \\ filter (size 1)} &\thead{\No of context filters\\ (size 2, size 3, size 4)} &\thead{Accuracy}\\
\hline
32 & 32 , 32 , 32 & 0.835 \\
\hline
32 & 64 , 64 , 64 & 0.821 \\
\hline
\hline
\end{tabular}
\hfill
\begin{tabular}{|*{3}{Sc|}}
\hline
\thead{\No of entity \\ filter (size 1)} &\thead{\No of context filters\\ (size 2, size 3, size 4)} & \thead{Accuracy}\\
\hline
512 & 32 , 32 , 32 & 0.910 \\
\hline
512 & 64 , 64 , 64 & 0.922 \\
\hline
\hline
\end{tabular}
\end{table}
\begin{table}[htbp]
\setlength\tabcolsep{4pt}\small
\caption{filter window size}
\label{tab:config_filternum}
\begin{tabular}{*{3}{c}}
\toprule
\thead{\No of entity \\ filter (size 1)} &\thead{\No of context filters\\ (size 2, size 3, size 4)} &\thead{Accuracy}\\
\cmidrule(lr){1-1} \cmidrule(lr){2-2} \cmidrule(lr){3-3}
32 & 32 , 32 , 32 & 0.835 \\
\addlinespace
32 & 64 , 64 , 64 & 0.821 \\
\bottomrule
\end{tabular}
\hfill
\begin{tabular}{*{3}{c}}
\toprule
\thead{\No of entity \\ filter (size 1)} &\thead{\No of context filters\\ (size 2, size 3, size 4)} & \thead{Accuracy}\\
\cmidrule(lr){1-1} \cmidrule(lr){2-2} \cmidrule(lr){3-3}
512 & 32 , 32 , 32 & 0.910 \\
\addlinespace
512 & 64 , 64 , 64 & 0.922 \\
\bottomrule
\end{tabular}
\end{table}
\begin{table}[htbp]
\setlength\tabcolsep{4pt}\small
\caption{filter window size}
\label{tab:config_filternum}
\begin{tabular}{*{3}{c}}
\toprule
\addlinespace[0pt]
\cmidrule{1-3}
\thead{\No of entity \\ filter (size 1)} &\thead{\No of context filters\\ (size 2, size 3, size 4)} &\thead{Accuracy}\\
\cmidrule(lr){1-1} \cmidrule(lr){2-2} \cmidrule(lr){3-3}
32 & 32 , 32 , 32 & 0.835 \\
\addlinespace
32 & 64 , 64 , 64 & 0.821 \\
\cmidrule{1-3}
\addlinespace[-2.7pt]
\bottomrule
\end{tabular}
\hfill
\begin{tabular}{*{3}{c}}
\toprule
\addlinespace[0pt]
\cmidrule{1-3}
\thead{\No of entity \\ filter (size 1)} &\thead{\No of context filters\\ (size 2, size 3, size 4)} & \thead{Accuracy}\\
\cmidrule(lr){1-1} \cmidrule(lr){2-2} \cmidrule(lr){3-3}
512 & 32 , 32 , 32 & 0.910 \\
\addlinespace
512 & 64 , 64 , 64 & 0.922 \\
\cmidrule{1-3}
\addlinespace[-2.7pt]
\bottomrule
\end{tabular}
\end{table}
\end{document}

\raggedright. I guess it will look better. – Johannes_B Aug 01 '16 at 08:38\RaggedRight. – Bernard Aug 01 '16 at 08:49